The rapid decline of California’s endangered delta smelt Hypomesus transpacificus has called for immediate and effective conservation actions. Since 2021, up to 92000 cultured delta smelt have been released annually into the Sacramento-San Joaquin River Delta, with ecological field surveys capturing both hatchery-produced (‘cultured’) and wild-spawned (‘wild’) individuals. Cultured fish now constitute the bulk of the catch, highlighting their critical role in conserving the species. Questions remain, however, regarding differences between cultured and wild individuals, their relative health, and how to accurately classify individuals collected in the field. We applied otolith-based tools to contrast the health and environmental histories of wild and cultured delta smelt collected in situ from 2019-2023. Specifically, we quantified differences in otolith development, otolith-somatic proportionality, ontogenetic growth, and otolith strontium isotope (87Sr/86Sr) geochemistry. We then developed mixture discriminant analysis models to identify cultured and wild individuals based on their geochemical profiles. Cultured and wild fish exhibited similar otolith-somatic proportionality, whereas cultured fish exhibited higher frequencies of abnormal (vateritic) otolith development. Growth varied ontogenetically in both groups; however, growth rates were highest in wild fish during the early life history and higher in cultured fish during later life stages. Geochemical profiles were distinct between groups, resulting in >95% classification success. Together, these results highlight the utility of otolith-based approaches for identifying wild and cultured delta smelt and quantifying differences in their health and environmental histories. Such data are key to understanding population dynamics and for informing the management and conservation of imperiled species.